Taxonomy Flashcards
Nomenclature
- Binomial system used to name all cellular organisms
- Names are descriptive and derived from Latin and Greek
What are stromatolites
Microbial mats consisting of layers of filamentous prokaryotes, sediments and extracellular matrix
Origin or cellular life: Theories
- Surface origin hypothesis
- Subsurface origin hypothesis
Surface origin hypothesis
- The first membrane-enclosed, self-replicating cells arose out of primordial soup rich in organic and inorganic compounds in ponds on Earth’s surface
- Dramatic temperature fluctuations (day/night) and mixing from meteor impacts, dust clouds, and storms argue against this hypothesis
Subsurface origin hypothesis
- Life originated in hydrothermal springs on the ocean floor
- Conditions would have been more stable
- Steady and abundant supply of energy (e.g., H 2 and H 2 S) was likely available at these sites
Origin of cellular life: Emergence steps
- Prebiotic chemsitry:
* Biological building blocks - Precellular life:
* RNA world
* Protein synthesis
* DNA - Early cellular life:
* Lipid bilayers - LUCA
- Diversification of Bacteria & Archaea
RNA world theory
First self-replicating system may have been RNA
* RNA can bind small molecules
* RNA has catalytic activity
* RNA can be copied like DNA
LUCA
Population of early cells from which
cellular life may have diverged into ancestors of modern-day Bacteria and Archaea
Origin of Life: Conditions
Early Earth was anoxic and much hotter than present day
2 methods of classification
- Phenetics: Overall similarity
- Phylogenetics: Evolutionary relationships
Phenetics: Rules
- All characteristics should be considered of equal importance
- Classification should be base on as many features as possible.
- Organisms should be grouped based on overall similarity
Similarity/Jaccard coefficient
S = # shared/total
Sj = # shared/(total - negative shared)
- 0.85 = species similarity
- 0.65 = genus similarity
Phenon
Group of organisms that have characters in common
Phylogenetics
- Fossil record
- Ribosomal RNA sequencing
- Multi-locus sequence typing
- Whole genome sequencing
Ribosomal RNA sequencing: Steps
- Amplification of the gene encoding SSU rRNA
- Sequencing of the amplified gene
- Analysis of sequence in reference to other sequences
SSU rRNA
- Contains conserved & variable region
- Evolutionary relationship
between 2 organisms = # of mutations in each region. - Few differences: closely related
- Many differences: loosely related
Multi-locus sequence typing (MLST)
- Method in which several different “housekeeping genes” from a species are sequenced and aligned to the respective sequences of other individuals of the same species
- Can distinguish between very closely related strains
Phylogenetic tree
Graphic illustration of the relationships among sequences
* Branch length = the number of changes that have occurred along that branch
* Branches = the order of descent & ancestry of the nodes
* Nodes: putative common ancestor
Polyphasic approach to taxonomy
- Phylogenetic analysis (SSU rRNA)
- Phentypic analysis (motility, capsule, virulence…)
- Genotypic analysis (presence/absence of specific genes)
Identification
- Comparison of its properties with those of organisms that have already been classified and named
- Dichotomous key
- Serotyping
Serotyping
Based on the binding of specific antibody to surface structure:
* LPS: O serotypes
* Capsule: K serotypes
* Flagella: H serotypes
* H1N1, Hemagglutinin 1, Neuraminidase 1
Positive reaction: agglutination
Ancient Vs Modern stromatolites
- Ancient stromatolites: Anoxygenic phototrophic filamentous bacteria
- Modern stromatolites: Oxygenic phototrophic cyanobacteri
